hey, I had a thought recently.... Satoshi Tajiri's original concept for Pocket Monsters was to recreate his childhood days of bug-catching. Catching for the sport, trading captures with other kids, and keeping captures for pets. Now animals are living creatures, and like us, they are capable of free-will, but for the most part, they're driven by instinct and much less intelligent than us. Because of this, they are treated as objects to an extent, and whether you like to admit it or not, when you go to the pet store (the concept of selling these creatures for profit being another key thing here), you're going because you want to add a doggy or a kitty to your possession (to say you want to make friends with a dog or cat would be incorrect, since you're still taking them into your custody).
Anyway, I think when Pocket Monsters was first made, they had this realistic concept of animals in mind. But, to take it one step further, Pokeballs were conceived to not only make the creatures portable, but as an added bonus, they brainwash (most, usually the weaker) Pokemon into being your loyal servants, servants which do the one thing you can do inside the boundaries of the game: battle. It was a simple program, there's no grooming the Pokemon, no interacting with them, nothing but getting involved in RPG-style fights. In all honesty, I wouldn't be surprised if all Pokemon were meant to have about as much personality as Ash's Pidgeotto (or a disobediant dog in the case of those few that don't follow commands). Sure, at the end of the game, Oak comments on how you won the Pokemon League because you love your Pokemon, but this was probably meant on the same level that people show affections when they care for animals in real life (though, that probably makes it sound like your rival beats and abuses his monsters). And since Pokemon could be treated as mere possessions, there was emphasis on trading them with human friends (or even making new friends. Japan has a lot of people, after all), or collecting a large number of them (sure, "gotta catch 'em all" is the dated English catchphrase, but the Japanese catchphrase, which still exists today, is "get Pokemon". Not collect all of them, but just gather lots of them, regardless of whether they're first befriended or not. This is why in the early days of the anime, characters would often use their number of catches for bragging rights).
The idea of Pokemon with more in-depth personalities only started to appear in mediums like the manga and anime, much later than the games, let alone the original planning of the games, and these personalities started to make them seem more human than the animals they actually are. I guess I'm getting at two things here. 1) Pokebots aren't really as bad as they're made out to be. Not that I'd intend to use them, but given the franchise's origins, it seems perfectly fine to focus on the human characters alone and make Pokemon little more than tools (don't anyone give me that "it's titled 'Pokemon' or 'Pocket Monsters', not 'Pokemon Trainers'" excuse. The title was obviously made to represent the creatures that live in the world. Humans are still the main characters, which go out and explore this world, gaining experience in tamings its monsters. It's also worth nothing that on the Japanese boxes to Red and Green version, as well as Blue and Pikachu versions later, there's a big banner which reads "The Pocket Monster Trainer", a good sign that emphasis is put on them). 2) Since Pokeballs are an instrument of the original gameplay mechanic, I wouldn't question their abilities to recall a Pokemon that's acting disobediant, even going on a rampage. For that matter, there's probably little reason to try to explain how they work. It's like trying to explain how mushrooms can turn Mario about 10 times his size. Explaining in your story is optional, but people honestly wouldn't care if it's explained or not since they're already familiar with the mechanic from their favorite games.